Efficacy of Using Environmental DNA (eDNA) to Detect Kirtland’s Snakes (Clonophis kirtlandii)

Environmental DNA (eDNA) surveys utilize DNA shed from animals in order to detect their presence. Since it was developed, this technique has been applied to numerous species across several taxa. In some cases, it has been shown to be superior to traditional survey methods at detecting rare or cryptic species. It allows for the detection of animals in low numbers and does not require direct capture of an animal. This allows eDNA to be more effective at detecting rare or cryptic species that require high survey effort to find. This often reduces survey costs as many eDNA samples can be collected quickly with little equipment required.

The Kirtland’s Snake (Clonophis kirtlandii) is a small Natricine snake endemic to the Midwest. It is a species of conservation concern since it is threatened throughout its range. Due to its cryptic and fossorial lifestyle, it is also a notoriously difficult snake to survey. This has resulted in a poor understanding of Kirtland’s Snake life history and population status. Applying eDNA surveys to this species may increase detection probability, offering a more efficient way to survey for them.

In this study, a quantitative PCR (qPCR) assay was designed and tested alongside traditional coverboard surveys. The assay had a limit of detection of 166 copies of Kirtland’s Snake DNA. In crayfish burrow sediment, eDNA was found to be detectable up to 10 days and may persist for up to 25 days. However, only one detection occurred out of 380 field samples. Coverboard surveys revealed temporal and spatial variation in Kirtland’s Snake abundance. More snakes were captured in the spring, during the first field season, and at the south coverboard transects. Kirtland’s Snake abundance was also found to be related to the presence of grass and herbaceous vegetation as well as close proximity to shrubs. Comparing survey methods, coverboards resulted in far better snake detection, suggesting that eDNA does not offer an advantage over traditional survey methods for this species.